[MMTK] Newby question

Konrad Hinsen hinsen at cnrs-orleans.fr
Mon Jul 14 14:47:58 EDT 2003


On Thursday 10 July 2003 10:25, Michiel Jan Laurens de Hoon wrote:

> homology modeling, I can create PDB files with the estimated structure
> of a mutated HIV protease.  With MMTK, I try to estimate the binding
>
> energy as follows:
>  >>> pdb = PDBMolecule('mutant.pdb')
>  >>> inhibitor = pdb.createMolecule('BLK')
>  >>> protease = Protein('mutant.pdb')

I suppose that's PDBConfiguration instead of PDBMolecule.

> Now the PDB file does not contain the hydrogen atoms.  Is there a way to
> add those to the protease and the inhibitor from MMTK?

For the protease that should have been done automatically by the Protein 
constructor. For any other molecule, e.g. your inhibitor, it can be done 
explicitly:

   inhibitor.findHydrogenPositions()

> This fails because the Amber94 force field parameters are missing for
> the inhibitor.  Are such parameters available somewhere?  I didn't find

It depends on the inhibitor... The Computational Chemistry List would be a 
good place to ask such a question.

> well-studied molecule.  Is it possible to mock up the interaction
> between the protease and the inhibitor?  Something quick and dirty is
> fine for what I am doing.

The most critical part of that interactions would be electrostatics, so you 
need decent partial charges for your inhibitor. The preferred way to obtain 
them is from ab initio calculations. Assuming you can do those, 
MMTK.ChargeFit can do the necessary fit for you.

Konrad.
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